From e36bd00bfd61582cd26e8c98d86a07ae0f2db49e Mon Sep 17 00:00:00 2001 From: jeffersonfparil Date: Mon, 24 Jun 2024 08:36:51 +1000 Subject: [PATCH] setting default to not remove phenotype outliers as we assume the user has taken steps to account for outliers in the phenotype data --- inst/exec_Rscript/config.txt | 12 ------------ inst/exec_Rscript/gp.R | 2 +- 2 files changed, 1 insertion(+), 13 deletions(-) diff --git a/inst/exec_Rscript/config.txt b/inst/exec_Rscript/config.txt index faeacbf..613a4a3 100644 --- a/inst/exec_Rscript/config.txt +++ b/inst/exec_Rscript/config.txt @@ -1,15 +1,3 @@ -GENOTYPE_DATA_RDS=/group/pasture/Jeff/gp/inst/exec_Rscript/input_tmp/test_geno.Rds -PHENOTYPE_DATA_TSV=/group/pasture/Jeff/gp/inst/exec_Rscript/input_tmp/test_pheno.tsv -KFOLDS=3 -NREPS=3 -DIR_OUT=/group/pasture/Jeff/gp/inst/exec_Rscript/output_tmp -SBATCH --job-name="AAA" -SBATCH --account="dbiopast1" -SBATCH --ntasks=1 -SBATCH --cpus-per-task=8 -SBATCH --mem=64G -SBATCH --time=0-2:0:00 - GENOTYPE_DATA_RDS=${DIR_SRC}/input/test_geno.Rds PHENOTYPE_DATA_TSV=${DIR_SRC}/input/test_pheno.tsv KFOLDS=2 diff --git a/inst/exec_Rscript/gp.R b/inst/exec_Rscript/gp.R index 0fa9977..7fcded8 100644 --- a/inst/exec_Rscript/gp.R +++ b/inst/exec_Rscript/gp.R @@ -27,7 +27,7 @@ parser$add_argument("--pheno-idx-col-id", dest="p parser$add_argument("--pheno-idx-col-pop", dest="pheno_idx_col_pop", type="integer", default=2, help="Column number in the phenotype file corresponding to the population/grouping names [default=2].") parser$add_argument("--pheno-idx-col-y", dest="pheno_idx_col_y", type="integer", default=3, help="Column number in the phenotype file corresponding to the numeric phenotype data [default=3].") parser$add_argument("--pheno-na-strings", dest="pheno_na_strings", type="character", default=c("", "-", "NA", "na", "NaN", "missing", "MISSING"), help="Strings of characters corresponding to missing data in the phenotype file [default=c('', '-', 'NA', 'na', 'NaN', 'missing', 'MISSING')].") -parser$add_argument("--pheno-bool-remove-outliers", dest="pheno_bool_remove_outliers", type="logical", default=TRUE, help="Remove outliers from the phenotype file [default=TRUE]?") +parser$add_argument("--pheno-bool-remove-outliers", dest="pheno_bool_remove_outliers", type="logical", default=FALSE, help="Remove outliers from the phenotype file [default=TRUE]?") parser$add_argument("--pheno-bool-remove-NA", dest="pheno_bool_remove_NA", type="logical", default=FALSE, help="Remove samples missing phenotype data in the phenotype file? [default=FALSE].") parser$add_argument("--bool-within", dest="bool_within", type="logical", default=TRUE, help="Perform within population k-fold cross-validation? [default=TRUE].") parser$add_argument("--bool-across", dest="bool_across", type="logical", default=FALSE, help="Perform across populations cross-validations? [default=FALSE].")